[gmx-users] Protein-Ligand in bilayer

[Abhishek Acharya]

For simulations using the Charmm36 params, using CHARMM-GUI is recommended.
Otherwise, you can also check out Justin's tutorial which is quite
instructive for beginners and provides a step by step method to build a
membrane protein system.

On Fri, Aug 10, 2018 at 2:24 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> Thank you.
>
> I wanna know of the alternative method to carry out this simulation. other
> than using charmm gui.
> thank you
>
> On Fri, Aug 10, 2018 at 2:07 PM, Abhishek Acharya <
> abhi117acharya at gmail.com>
> wrote:
>
> > I see. I have not used charmm-gui for building system as complex as
> yours,
> > so I can't comment on the issue. But this is a problem specific to
> > charmm-gui. I suggest you contact the authors of the web-service
> directly.
> >
> > Abhishek
> >
> > On Fri, Aug 10, 2018 at 10:07 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > Hi.
> > >
> > > Thank you.
> > >
> > > But the system (protein ligand) is being constructed in charm gui input
> > > generator, where it automatically compare the complex pdb and ligand
> mol2
> > > file ( which will Ben uploaded ).
> > >
> > > On Thu, 9 Aug 2018 at 11:24 PM, Abhishek Acharya <
> > abhi117acharya at gmail.com
> > > >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > >
> > > >
> > > > > It look so complicated to carry out a protein ligand simulation in
> > > Lipid
> > > > > bilayer system using charmm ff. I have a ligand with 27 atoms (
> > > includes
> > > > > Hydrogen ). The initial structure (monomer)  is simulated in popc
> > > > > constructed using charmm gui web page. To construct the same for
> the
> > > > > portein-ligand complex is too tedious and very problematic.
> > > > > The protein-ligand complex is constructed using auto dock from the
> > mol2
> > > > > file download from Zinc database. The complex structure then is
> > > uploaded
> > > > to
> > > > > charmm gui and the atom number varies with the mol2 file and pdb
> > file.
> > > I
> > > > > find no way to change the atom order or numbering.
> > > > >
> > > >
> > > >
> > > > Why this is a problem? Whatever the numbering you get in the output,
> > you
> > > > can always renumber the atoms using editconf. Check gmx editconf -h.
> > > > --
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> > > --
> > > *Regards,*
> > > *Rahul *
> > > --
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>
>
> --
> *Regards,*
> *Rahul *
> --
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